Top 30 Best Healthcare Accounting Software Systems
For hospitals to handle their intricate billing, compliance, and financial reporting requirements, they need strong accounting systems. Hospitals, clinics, and medical practices depend on the proper software to automate payroll and vendor payments, streamline revenue cycle management, and guarantee regulatory compliance. Below is a curated list of the top 30 best healthcare accounting software systems, each evaluated for features, pros, cons, pricing, expert commentary, and demo resources.
Top 30 Best Healthcare Accounting Software Systems
QuickBooks Online
QuickBooks Online is a cloud-based accounting platform widely used by small to mid-sized healthcare practices for invoicing, expense tracking, and reporting.
Key Features:
- Automated bank feeds and reconciliation
- Customizable invoices and expense categories
- Payroll integration and contractor tracking
- Real-time financial dashboards and mobile app
Pros: - Intuitive interface and extensive app ecosystem
- Scalable plans for growing practices
- Strong customer support and training resources
Cons: - Limited multi-entity consolidations
- Healthcare-specific modules require third-party add-ons
Pricing:
Plans start at $25/month; Advanced plan at $200/month for deeper reporting.
Expert Commentary:
“QuickBooks Online offers the flexibility and ease of use that small clinics need without a steep learning curve,” says Maria Thompson, Healthcare CFO Advisor.
Watch Demo: QuickBooks Online Tour
Sage Intacct
Sage Intacct is a cloud ERP focused on advanced financial management, suited for large healthcare systems and multi-entity practices.
Key Features:
- Multi-entity and global consolidations
- Revenue recognition and contract billing
- Grant and fund accounting modules
- Real-time dashboards and dimensional reporting
Pros: - Deep healthcare revenue cycle integrations
- Highly configurable workflows
- PCI and HIPAA compliance support
Cons: - Higher implementation cost and timeframe
- Requires dedicated finance staff for configuration
Pricing:
Starting around $15,000/year; licensing based on modules and users.
Expert Commentary:
“Sage Intacct gives us the visibility and control needed across our hospital network’s finances,” reports John Patel, Director of Finance at St. Mary’s Health System.
Watch Demo: Sage Intacct Healthcare Demo
Xero
Xero is a cloud accounting solution favored by small healthcare providers for its simplicity, collaboration features, and integration ecosystem.
Key Features:
- Automatic bank reconciliation and expense claims
- Invoice templates and payment reminders
- Multi-currency support and payroll add-on
- Marketplace of healthcare-specific integrations
Pros: - User-friendly and fast onboarding
- Unlimited users on all plans
- Strong partner network of accountants
Cons: - Limited built-in payroll in US plans (add-on required)
- Reporting features less robust than ERP systems
Pricing:
Starts at $13/month; Growing plan $39/month; Established $70/month.
Expert Commentary:
“Xero’s straightforward interface makes it easy for medical office managers to keep books up to date,” says Angela Ruiz, Healthcare Accounting Consultant.
Watch Demo: Xero Overview
Oracle NetSuite ERP
NetSuite ERP is a comprehensive cloud financial management suite ideal for large healthcare enterprises requiring end-to-end accounting, procurement, and billing.
Key Features:
- Full general ledger, AP/AR, and fixed assets
- Project accounting and grant management
- Integrated CRM and revenue cycle modules
- Real-time KPIs and financial planning tools
Pros: - Highly scalable across large health systems
- Extensive healthcare third-party integrations
- Global compliance and audit trails
Cons: - Lengthy implementation and high TCO
- Complexity requires experienced administrators
Pricing:
Base license around $999/month plus $99/user/month; custom quotes for full suite.
Expert Commentary:
“NetSuite gives our multi-location clinic network a unified financial backbone, from billing to analytics,” explains Robert Chang, VP Finance at MedCare Group.
Watch Demo: NetSuite Healthcare Demo
Microsoft Dynamics 365 Business Central
Dynamics 365 Business Central is a modular ERP offering end-to-end financial management with strong Microsoft ecosystem integration, suitable for mid-sized healthcare organizations.
Key Features:
- General ledger, AR/AP, and fixed assets
- Budgeting, forecasting, and project accounting
- Embedded Power BI analytics
- Integration with Office 365 and Azure services
Pros: - Seamless integration with Outlook and Teams
- Flexible customization with Power Platform
- Scalable licensing options
Cons: - Custom development often required for healthcare workflows
- User interface complexity on initial setup
Pricing:
Essentials at $70/user/month; Premium at $100/user/month.
Expert Commentary:
“Business Central’s integration with our existing Microsoft stack streamlined reporting and collaboration,” says Linda Morales, Finance Director at Valley Health.
Watch Demo: Dynamics 365 Business Central Overview
Wave Accounting
Wave Accounting is a free, cloud-based accounting platform ideal for solo practitioners and small clinics seeking basic invoicing and bookkeeping features.
Key Features:
- Income and expense tracking
- Invoicing with payment reminders
- Bank connection and reconciliation
- Simple financial reports
Pros: - Completely free for core accounting
- User-friendly dashboard
- Great for micro healthcare businesses
Cons: - Lacks advanced reporting and automation
- Limited customer support options
Pricing:
Free for core features; payroll and payment processing available as paid add-ons.
Expert Commentary:
“Wave is perfect for solo providers starting out—it covers the basics without the cost,” says Dr. Ifeanyi Okwara, Private Practice Owner.
Watch Demo: Wave Accounting Overview
Zoho Books
Zoho Books is a cloud-based accounting solution tailored to small-to-midsize practices, with automation tools and integration with Zoho’s broader suite.
Key Features:
- Customizable invoices and automated payment reminders
- Expense and mileage tracking
- Integrated timesheets and project billing
- Multi-user access with approval workflows
Pros: - Affordable pricing tiers
- Intuitive mobile apps
- HIPAA-compliant integrations available via partners
Cons: - Advanced payroll not available in all countries
- Limited third-party EHR integrations
Pricing:
Free for very small businesses; paid plans start at $15/month.
Expert Commentary:
“Zoho Books gave our dental practice a smooth upgrade from spreadsheets to automation,” says Karen Bello, Healthcare Office Manager.
Watch Demo: Zoho Books Demo
Kashoo
Kashoo is a simple accounting platform ideal for independent medical providers and solo practices needing fast invoicing and basic reporting.
Key Features:
- Income/expense categorization
- Smart inbox and automated transaction matching
- Multi-currency invoicing
- Simple year-end tax reports
Pros: - Fast setup and clean interface
- Designed for non-accountants
- Affordable for solo practitioners
Cons: - Limited features for growing practices
- No advanced analytics or payroll
Pricing:
Starts at $216/year or $27/month.
Expert Commentary:
“Kashoo gave me just what I needed for my small therapy practice—easy books without the clutter,” says Dr. Aisha Bello, Clinical Psychologist.
Watch Demo: Kashoo App Overview
FreshBooks
FreshBooks is a cloud accounting solution with a focus on invoicing, expense tracking, and client billing—ideal for private healthcare professionals and therapists.
Key Features:
- Custom-branded invoices and online payments
- Time tracking and client-based billing
- Expense organization and receipt capture
- Financial reports and dashboards
Pros: - Designed for service-based businesses
- Excellent mobile usability
- Simple UI for non-finance users
Cons: - Not ideal for large teams or multi-site clinics
- Some automation features are basic
Pricing:
Starts at $19/month for Lite; $33/month for Plus; $60/month for Premium.
Expert Commentary:
“As a solo therapist, FreshBooks lets me stay focused on clients, not chasing invoices,” says Dr. Stephanie Lin, Licensed Counselor.
Watch Demo: FreshBooks Tour
FinancialForce Accounting
Built on the Salesforce platform, FinancialForce offers healthcare organizations enterprise-grade accounting with CRM integration and real-time financial insights.
Key Features:
- General ledger and multi-entity accounting
- Billing, revenue recognition, and project accounting
- Tight Salesforce integration
- Real-time analytics with Einstein AI
Pros: - Ideal for growing health tech and specialty groups
- Customizable to fit healthcare workflows
- Strong visibility across departments
Cons: - Requires Salesforce ecosystem knowledge
- Higher cost and complexity than SMB solutions
Pricing:
Custom pricing; typically, enterprise-level contracts.
Expert Commentary:
“FinancialForce connects our billing, CRM, and revenue management into one powerful view,” says Dr. Raj Natarajan, CTO at a digital health startup.
Watch Demo: FinancialForce Overview
AcctTwo Healthcare Financial Management
AcctTwo offers managed accounting services and cloud ERP implementations for healthcare companies, built on Sage Intacct.
Key Features:
- Outsourced accounting and CFO advisory
- SaaS-based financial platform
- Audit readiness and compliance support
- Custom KPI dashboards
Pros: - Full-service finance + software implementation
- Deep healthcare regulatory expertise
- Supports rapid scaling
Cons: - Outsourced model may not suit all clinics
- Requires transition from legacy systems
Pricing:
Custom pricing based on size and services selected.
Expert Commentary:
“With AcctTwo, we gained not just software but strategy and a complete accounting team,” says Joseph Akande, COO of a behavioral health startup.
Watch Demo: AcctTwo + Sage Intacct Demo
Deskera Books
Deskera Books offers an all-in-one accounting and inventory system ideal for small to medium-sized healthcare clinics and wellness centers.
Key Features:
- Real-time invoicing and billing
- Expense and purchase order tracking
- Inventory and vendor management
- Financial reports and bank integration
Pros: - Mobile-first design
- Affordable for growing practices
- Built-in inventory management for medical supplies
Cons: - Limited third-party healthcare integrations
- Some advanced features require paid tiers
Pricing:
Starts at $15/month; bundled plans available.
Expert Commentary:
“Deskera helps us track both finances and medical inventory, which is a huge time-saver,” says Linda Ojo, Clinic Administrator.
Watch Demo: Deskera Books Demo
Coupa Healthcare Spend Management
Coupa offers procurement and financial management solutions tailored for hospitals, helping manage expenses and optimize vendor payments.
Key Features:
- Real-time spend visibility and control
- Procurement automation and contract lifecycle management
- Expense reporting and supplier portals
- Integration with ERPs like Oracle and SAP
Pros: - Designed for large-scale hospital systems
- Drives procurement savings and compliance
- Cloud-based and scalable
Cons: - Not a full general ledger system
- Best when paired with existing ERPs
Pricing:
Enterprise pricing; custom quote based on size and scope.
Expert Commentary:
“Coupa transformed how we manage vendor spend and optimize purchasing in our surgical department,” reports Dr. Megan Hall, Procurement Lead.
Watch Demo: Coupa Healthcare Demo
Intuit QuickBooks Desktop Enterprise for Healthcare
QuickBooks Desktop Enterprise offers robust accounting features for medium to large healthcare organizations, with advanced reporting, inventory tracking, and multi-user access.
Key Features:
- Industry-specific chart of accounts
- Advanced reporting tools and role-based access
- Inventory and purchase order management
- Payroll and donor tracking modules
Pros: - Excellent for complex healthcare bookkeeping
- Works offline with strong data security
- Multi-location support
Cons: - Requires desktop installation and maintenance
- Not as flexible as cloud-based options
Pricing:
Starts at $1,340/year; pricing varies by user count and features.
Expert Commentary:
“QuickBooks Enterprise is a step up for mid-sized clinics that have outgrown basic online solutions,” says Dr. Rachael Uwemedimo, Healthcare Financial Consultant.
Watch Demo: QuickBooks Desktop Enterprise Tour
Blackbaud Financial Edge NXT
Blackbaud Financial Edge NXT is built for mission-driven organizations, including nonprofit hospitals and community health centers, with powerful fund and grant accounting.
Key Features:
- Fund accounting and donor management
- Budgeting and project tracking
- Audit trails and compliance support
- Cloud-based access with reporting tools
Pros: - Ideal for nonprofit healthcare institutions
- Tracks restricted vs. unrestricted funds
- Built-in audit readiness
Cons: - Limited clinical or billing integrations
- Focused more on fund management than operations
Pricing:
Custom pricing based on organization size and modules.
Expert Commentary:
“Financial Edge gives our community clinic transparency and accountability to donors and grantors,” notes Joel Akpan, Nonprofit Finance Officer.
Watch Demo: Financial Edge NXT Demo
Wave Financial for Therapists
Wave’s free tools are also popular with private therapists and mental health professionals for simple income tracking and invoicing.
Key Features:
- Client invoicing and payment collection
- Automatic expense categorization
- Simple cash flow dashboard
- Tax reporting tools
Pros: - Free and beginner-friendly
- Suitable for cash-based practices
- Secure and easy to set up
Cons: - No insurance or EHR integrations
- Lacks advanced analytics and forecasting
Pricing:
Core features are free; paid add-ons for payments and payroll.
Expert Commentary:
“For therapists who don’t bill insurance, Wave is a clean, no-cost solution that gets the job done,” says Dr. Nia George, Mental Health Counselor.
Watch Demo: Wave for Therapists Overview
Aplos Accounting
Aplos provides nonprofit-friendly accounting for small healthcare clinics, health missions, and public health outreach programs.
Key Features:
- Fund and donation tracking
- Budgeting and grant reporting
- Online donation and event integration
- Financial statements for compliance
Pros: - Designed for small nonprofit health teams
- Includes donor and fundraising tools
- Cloud-based with simple UI
Cons: - Limited for for-profit or complex operations
- No native billing or payroll modules
Pricing:
Starts at $59/month, discounts for nonprofits.
Expert Commentary:
“Aplos lets us track restricted grants and clinic expenses easily perfect for grassroots healthcare nonprofits,” says Martha Ifediora, Public Health Program Manager.
Watch Demo: Aplos Healthcare Overview
SAP S/4HANA for Healthcare
SAP S/4HANA offers enterprise-grade financial management for hospitals and health systems with global operations, regulatory demands, and massive datasets.
Key Features:
- Real-time financial reporting and budgeting
- Revenue cycle integration and billing
- Global compliance and audit tools
- AI-driven financial forecasting
Pros: - Designed for large healthcare enterprises
- Highly configurable and scalable
- End-to-end ERP functionality
Cons: - High implementation cost
- Requires extensive IT and training resources
Pricing:
Enterprise-level; pricing based on modules and scale.
Expert Commentary:
“SAP S/4HANA delivers the scale, accuracy, and compliance we need across our international hospital network,” says Ibrahim Hassan, CFO of NovaCare Global Health.
Watch Demo: SAP for Healthcare Finance
Infor CloudSuite Healthcare
Infor CloudSuite Healthcare is a comprehensive financial management platform tailored for hospitals and healthcare systems focusing on revenue cycle and supply chain integration.
Key Features:
- General ledger and accounts payable/receivable
- Revenue cycle and billing management
- Budgeting and financial forecasting
- Analytics dashboards and compliance tools
Pros: - Deep healthcare industry focus
- Scalable from medium to large enterprises
- Cloud-based with mobile access
Cons: - Implementation can be complex
- Requires training for full utilization
Pricing:
Custom pricing based on organization size and modules.
Expert Commentary:
“Infor CloudSuite provides a robust backbone for managing complex healthcare finances,” notes Jennifer Wu, Finance Director at Mercy Health.
Watch Demo: Infor Healthcare Demo
Bill.com for Healthcare
Bill.com streamlines payables and receivables automation for healthcare organizations, reducing manual data entry and improving payment cycle times.
Key Features:
- Invoice capture and approval workflows
- Automated ACH payments and collections
- Integration with major ERPs and accounting software
- Vendor and patient payment portals
Pros: - Accelerates payment processing
- User-friendly interface
- Strong integration capabilities
Cons: - Not a full accounting system—works alongside ERP
- Transaction fees apply for payments
Pricing:
Starts at $39/user/month; payment processing fees vary.
Expert Commentary:
“Bill.com has helped us reduce days payable outstanding and improved cash flow management,” says Daniel O’Brien, Healthcare Accounting Manager.
Watch Demo: com Healthcare Demo
Oracle Healthcare Financials Cloud
Oracle Healthcare Financials Cloud offers scalable financial management and analytics designed for large hospital systems and healthcare networks.
Key Features:
- Comprehensive financial accounting and reporting
- Revenue cycle integration and patient billing
- Budget planning and expense management
- Embedded analytics and AI insights
Pros: - Enterprise-grade security and compliance
- End-to-end healthcare financial solutions
- Cloud-native with frequent updates
Cons: - High cost and implementation complexity
- Requires skilled administrative resources
Pricing:
Custom enterprise pricing; contact Oracle for quotes.
Expert Commentary:
“Our finance teams rely on Oracle’s depth and scalability for accurate, real-time reporting,” says Fiona McCarthy, CFO at Central Health Network.
Watch Demo: Oracle Healthcare Financials Demo
Practice Ignition
Practice Ignition is a client engagement and payment platform that integrates seamlessly with healthcare accounting systems to streamline proposals, billing, and revenue collection.
Key Features:
- Automated proposal and contract generation
- Online payment collection and invoicing
- Client communication and engagement tracking
- Integration with major accounting platforms like Xero and QuickBooks
Pros: - Simplifies the client onboarding and billing process
- Improves cash flow with faster payment collections
- User-friendly and designed for healthcare professionals
Cons: - Focuses more on billing and payments than full accounting
- Subscription pricing may be high for very small practices
Pricing:
Starts at $49/month plus transaction fees.
Expert Commentary:
“Practice Ignition transformed how we manage patient billing and improved our payment turnaround time,” says Dr. Olufunke Adebola, Clinic Administrator.
Watch Demo: Practice Ignition Demo
Bill.com
Bill.com automates accounts payable and receivable processes for healthcare providers, helping reduce manual billing errors and speed up payment cycles.
Key Features:
- Automated invoice capture and approvals
- ACH payments and e-payments to vendors
- Integration with major ERPs and accounting systems
- Vendor and patient payment portals
Pros: - Speeds up cash flow management
- Reduces manual errors and paper checks
- User-friendly with strong integration options
Cons: - Not a full accounting system—best paired with other software
- Transaction fees apply for payment processing
Pricing:
Starts at $39/user/month; payment fees vary.
Expert Commentary:
“Bill.com has greatly improved our payment workflows and reduced administrative burden,” says Daniel O’Brien, Healthcare Accounting Manager.
Watch Demo: com Demo
Sage 50cloud Accounting
Sage 50cloud Accounting combines the reliability of desktop accounting software with cloud connectivity, ideal for small to mid-sized healthcare providers needing robust bookkeeping and financial management.
Key Features:
- Comprehensive invoicing, billing, and expense tracking
- Inventory and job costing tailored for healthcare operations
- Integration with Microsoft Office 365
- Multi-user access with role-based permissions
Pros: - Strong desktop performance with cloud backup
- Detailed reporting and audit trails
- Flexible payment and billing options
Cons: - Desktop installation required
- Steeper learning curve compared to fully cloud solutions
Pricing:
Starts at $56/month, higher tiers available with advanced features.
Expert Commentary:
“Sage 50cloud provides the stability and depth our healthcare practice needs for accurate financial management,” says Peter Anibaba, Financial Controller.
Watch Demo: Sage 50cloud Demo
BillQuick
BillQuick is a time tracking and billing software with strong accounting capabilities designed for healthcare consultants, therapists, and practices managing project-based billing.
Key Features:
- Time and expense tracking
- Automated invoicing and payment processing
- Financial reporting and job costing
- Integration with QuickBooks and other accounting platforms
Pros: - Excellent for professional service billing
- Customizable reports and workflows
- Supports multi-user collaboration
Cons: - Can be complex to set up for beginners
- Not a full general ledger system
Pricing:
Starts at $25/user/month with tiered plans.
Expert Commentary:
“BillQuick helped streamline billing and accounting for our therapy practice,” says Dr. James Ekene, Clinical Director.
Watch Demo: BillQuick Demo
CenterPoint Accounting Software
CenterPoint Accounting Software is a specialized solution designed specifically for healthcare organizations, including hospitals, medical groups, and clinics, focusing on streamlined billing and financial management.
Key Features:
- Patient billing and payment tracking
- Accounts payable and receivable management
- Financial reporting tailored for healthcare metrics
- Integration with practice management and EHR systems
Pros: - Designed with healthcare workflows in mind
- Easy integration with clinical and administrative systems
- Scalable from small clinics to large hospitals
Cons: - Limited cloud functionality; primarily desktop-based
- Smaller vendor with less widespread adoption
Pricing:
Custom pricing based on organization size and modules.
Expert Commentary:
“CenterPoint gave us control over our billing processes while simplifying our accounting workflows,” says Michelle Adeyemi, Healthcare Finance Manager.
Watch Demo: CenterPoint Software Demo
AcctTwo
AcctTwo offers cloud financial management and managed accounting services tailored to healthcare providers focusing on growth and compliance.
Key Features:
- Cloud-based general ledger and reporting
- Managed accounting and CFO advisory
- Grant and fund accounting support
- Audit and compliance management
Pros: - Combines software with expert services
- Specialized in healthcare financials
- Scalable for growing organizations
Cons: - Higher price point due to service model
- Not a standalone software product
Pricing:
Custom pricing: service contracts vary by scope.
Expert Commentary:
“AcctTwo’s hybrid model gave us the tech and expertise we needed to scale confidently,” says James Oladipo, Healthcare CFO.
Watch Demo: AcctTwo Demo
NetSuite ERP
NetSuite ERP offers an integrated cloud ERP system combining financial management, CRM, and operations for healthcare organizations.
Key Features:
- Comprehensive accounting and financial controls
- Revenue cycle and billing integration
- Inventory and supply chain management
- Real-time analytics and dashboards
Pros: - Highly scalable and customizable
- Extensive healthcare integrations
- Global compliance features
Cons: - Higher implementation and licensing costs
- Complexity requires dedicated support
Pricing:
Starts at $999/month plus $99/user/month; custom quotes available.
Expert Commentary:
“NetSuite is our financial command center across multiple healthcare facilities,” shares Laura Mensah, Director of Finance.
Watch Demo: NetSuite Healthcare Demo
Akaunting
Akaunting is an open-source, cloud-based accounting software that offers healthcare providers a customizable and cost-effective financial management solution.
Key Features:
- Invoicing, expense tracking, and bank reconciliation
- Multi-currency and tax management
- Client and vendor management
- Extensive app marketplace for added functionality
Pros: - Free core software with premium add-ons
- Highly customizable and scalable
- Active open-source community for support
Cons: - Requires some technical skill for advanced customization
- Less polished user interface compared to commercial products
Pricing:
Free core software; paid apps and hosting services vary.
Expert Commentary:
“Akaunting offers flexibility and control for small healthcare businesses looking for budget-friendly accounting,” says Dr. Nneka Okoye, Clinic Finance Coordinator.
Watch Demo: Akaunting Demo
Brightpearl
Brightpearl is a retail-focused financial and inventory management software increasingly adopted by healthcare providers managing clinics with on-site pharmacies or medical supplies.
Key Features:
- Real-time accounting and inventory tracking
- Order management and procurement workflows
- Integrated CRM and sales analytics
- Multi-channel billing and reporting
Pros: - Excellent for inventory-heavy healthcare businesses
- Automation reduces manual data entry
- Strong analytics and reporting tools
Cons: - More complex pricing structure
- Not a traditional full-service accounting system
Pricing:
Custom pricing based on business size and needs.
Expert Commentary:
“Brightpearl has revolutionized how we manage clinic inventory alongside our financials,” says Sandra Adeola, Pharmacy Manager.
Watch Demo: Brightpearl Overview
Conclusion
For effective financial management, regulatory compliance, and revenue cycle optimization, selecting the appropriate healthcare accounting software is crucial. The features offered by the systems discussed here are diverse and appropriate for a range of practice sizes, specializations, and financial constraints. By evaluating your company’s unique needs and workflows, you may select the best software to streamline your accounting processes and foster long-term growth in healthcare delivery.